The Chlamydomonas genome: sequencing the roots of plants

The genome of a single celled green algae is completed, providing greater …

The latest in genome sequencing was published yesterday in Science. The organism in question, Chlamydomonas reinhardtii, is a rather unassuming creature: a single-celled, soil-dwelling green alga. But the genome is big news because of its evolutionary position, as Chlamy (as it's known to afficionados) split off from the rest of plants very early in their history. As a result, it shares a number of features, including two whip-like flagella, with animal cells. So the Chlamy genome provides some perspective on the common traits of both types of multicellular eukaryotes: plants and animals.

The genome itself is nothing unusual, aside from having a bias towards G/C base pairs. It totals about 121 Megabases, distributed among 17 chromosomes, with roughly 15,000 genes scattered among the typical collections of transposable DNA fragments. There seem to be an abundance of cell-surface transporters in the genome, which the authors ascribe to its need to outcompete everything else living in the soil for resources and nutrients.

What's important about the Chlamy genome is the perspective it provides on all the other ones we have completed. Chlamy occupies a rather distinct position on the tree of life. It's obviously a plant, as it contains a chloroplast and can engage in photosynthesis. But it split off from the rest of plants very shortly after that ability evolved via the endosymbiosis of a photosynthesizing bacteria. Its retained at least one property of the common ancestor of plants and animals: the flagella that it uses to propel itself, which is largely the same as the cilia that help keep our lungs clear. Meanwhile, it appears to have some unique properties, such as an eyespot that it uses to sense the light it needs to photosynthesize.

The overlap of shared genes reflects this. Chlamy shares about 2,300 gene families with both plants and animals, another 1,900 with plants alone, and a full 700 gene families that other plants don't have, but humans do. The authors also did full genome comparisons with dozens of organisms to identify the genes involved in common traits. For example, the "green cut" of genes associated with photosynthetic plastids comprised 90 proteins; over 70 percent of these had equivalents in cyanobacteria, which had previously been identified as the source of chloroplasts.

A similar analysis was done to identify the "cilia cut," which identified the proteins involved in creating the tails that Chlamy uses for both propulsion and cell signaling, which are absent in multicellular green plants. Apparently, it takes at least 190 types of proteins for either humans or Chlamy to make a cilia. That cut was then sliced a second way. Some animals, notably the lab worm C. elegans, do not use moving cilia, but simply produce them to help with cell signaling. Based on the genome comparisons, it's estimated that 62 proteins are sufficient to build a sensory cilia; the rest are needed to make it move.

As for the eye spot, it appears to be an outgrowth of structures that manage the production and trafficking of lipids and pigments in most plants. Many of the proteins known to reside there appear generally in plants, where some have been associated with things like carotene production. Given that any attempts at biofuel production using algae will probably involve trafficking hydrocarbons, this may be where we'll need to intervene.

To wrap up, I'm going to get a delve a bit into the philosophy of science and criticisms of evolution; those of you who wish to sit out of the debate can stop reading here, safe in the knowledge that the Chlamydomonas genome has provided new insights into the origin of plants and their last common ancestor with animals.

Those of you who follow the debate over evolution (which sporadically breaks out in these forums) are probably aware that many of its critics claim that the theory is not testable; we can't go back in time and see how things actually did evolve. But evolution, like any science with a historical component, is scientific because its reconstructions of the past make predictions about how the world should look now. In that sense, the genome sequence of Chlamydomonas was one big test of evolution. Based on the known properties of plants in general and Chlamy in specific, we had already predicted that Chlamy shared properties with animals, but it was closer to plants, and thus its chloroplast was derived from cyanobacteria. There are absolutely no surprises in the sequence—everything looks as we expected—but met expectations are the product of a successful theory passing yet another test.

Another frequent critique of evolution is that it doesn't have practical applications. The insights into cilia, especially their signaling function, provided by this evolutionary study would suggest otherwise. Those functions are conserved in humans, where the signaling pathways that use cilia have been implicated in human health. Look into the birth defects associated with faulty Hedgehog signaling, or cancers linked to the Patched and Gli genes carefully, and you'll find that all of these proteins require an intact cilia in order to function normally. Anything we learn about cilia from the comparisons with Chlamy has the potential to help our understanding of these diseases.

The fact that all of that comes out of the genome of a close cousin of pond scum is pretty amazing.